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https://git.gfz-potsdam.de/naaice/poet.git
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use better communicator creation
This commit is contained in:
Max Lübke
parent
b96131fa71
commit
b85575a69b
340
src/kin.cpp
340
src/kin.cpp
@ -100,22 +100,13 @@ int main(int argc, char *argv[]) {
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/*Create custom Communicator with all processes except 0 (the master) for DHT
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* storage*/
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// only needed if strategy == 0, but done anyway
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MPI_Group dht_group, group_world;
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MPI_Comm dht_comm;
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int *process_ranks;
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// make a list of processes in the new communicator
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process_ranks = (int *)malloc(world_size * sizeof(int));
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for (int I = 1; I < world_size; I++) process_ranks[I - 1] = I;
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// get the group under MPI_COMM_WORLD
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MPI_Comm_group(MPI_COMM_WORLD, &group_world);
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// create the new group
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MPI_Group_incl(group_world, world_size - 1, process_ranks, &dht_group);
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// create the new communicator
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MPI_Comm_create(MPI_COMM_WORLD, dht_group, &dht_comm);
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free(process_ranks); // cleanup
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if (world_rank == 0) {
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MPI_Comm_split(MPI_COMM_WORLD, MPI_UNDEFINED, world_rank, &dht_comm);
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} else {
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MPI_Comm_split(MPI_COMM_WORLD, 1, world_rank, &dht_comm);
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}
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// cout << "Done";
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// if (cmdl[{"help", "h"}]) {
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@ -430,188 +421,187 @@ int main(int argc, char *argv[]) {
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master.run();
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}
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// MDL master_iteration_end just writes on disk state_T and
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// state_C after every iteration if the cmdline option
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// --ignore-results is not given (and thus the R variable
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// store_result is TRUE)
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R.parseEvalQ("mysetup <- master_iteration_end(setup=mysetup)");
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// MDL master_iteration_end just writes on disk state_T and
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// state_C after every iteration if the cmdline option
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// --ignore-results is not given (and thus the R variable
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// store_result is TRUE)
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R.parseEvalQ("mysetup <- master_iteration_end(setup=mysetup)");
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// cummul_transport += trans.getTransportTime();
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// cummul_chemistry += master.getChemistryTime();
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// cummul_transport += trans.getTransportTime();
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// cummul_chemistry += master.getChemistryTime();
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cout << endl
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<< "CPP: End of *coupling* iteration " << iter << "/" << maxiter
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<< endl
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<< endl;
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cout << endl
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<< "CPP: End of *coupling* iteration " << iter << "/" << maxiter
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<< endl
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<< endl;
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// master_send.push_back(master.getSendTime(), "it_" + to_string(iter));
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// master_recv.push_back(master.getRecvTime(), "it_" + to_string(iter));
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// master_send.push_back(master.getSendTime(), "it_" + to_string(iter));
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// master_recv.push_back(master.getRecvTime(), "it_" + to_string(iter));
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for (int i = 1; i < params.world_size; i++) {
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MPI_Send(NULL, 0, MPI_DOUBLE, i, TAG_DHT_ITER, MPI_COMM_WORLD);
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for (int i = 1; i < params.world_size; i++) {
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MPI_Send(NULL, 0, MPI_DOUBLE, i, TAG_DHT_ITER, MPI_COMM_WORLD);
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}
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MPI_Barrier(MPI_COMM_WORLD);
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} // END SIMULATION LOOP
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cout << "CPP: finished simulation loop" << endl;
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sim_end = MPI_Wtime();
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cout << "CPP: start timing profiling" << endl;
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R.parseEvalQ("profiling <- list()");
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R["simtime"] = sim_end - sim_start;
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R.parseEvalQ("profiling$simtime <- simtime");
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trans.end();
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if (params.world_size == 1) {
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master.ChemSim::end();
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} else {
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master.end();
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}
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MPI_Barrier(MPI_COMM_WORLD);
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// Rcpp::NumericVector phreeqc_time;
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// Rcpp::NumericVector dht_get_time;
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// Rcpp::NumericVector dht_fill_time;
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// Rcpp::IntegerVector phreeqc_counts;
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// Rcpp::NumericVector idle_worker;
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} // END SIMULATION LOOP
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// int phreeqc_tmp;
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cout << "CPP: finished simulation loop" << endl;
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// timings = (double *)calloc(3, sizeof(double));
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sim_end = MPI_Wtime();
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// int dht_hits = 0;
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// int dht_miss = 0;
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// int dht_collision = 0;
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cout << "CPP: start timing profiling" << endl;
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// if (params.dht_enabled) {
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// dht_hits = 0;
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// dht_miss = 0;
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// dht_collision = 0;
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// dht_perfs = (uint64_t *)calloc(3, sizeof(uint64_t));
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// }
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R.parseEvalQ("profiling <- list()");
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// double idle_worker_tmp;
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R["simtime"] = sim_end - sim_start;
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R.parseEvalQ("profiling$simtime <- simtime");
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// for (int p = 0; p < params.world_size - 1; p++) {
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// /* ATTENTION Worker p has rank p+1 */
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// /* Send termination message to worker */
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// MPI_Send(NULL, 0, MPI_DOUBLE, p + 1, TAG_FINISH, MPI_COMM_WORLD);
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trans.end();
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// MPI_Recv(timings, 3, MPI_DOUBLE, p + 1, TAG_TIMING, MPI_COMM_WORLD,
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// MPI_STATUS_IGNORE);
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// phreeqc_time.push_back(timings[0], "w" + to_string(p + 1));
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if (params.world_size == 1) {
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master.ChemSim::end();
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} else {
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master.end();
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// MPI_Recv(&phreeqc_tmp, 1, MPI_INT, p + 1, TAG_TIMING, MPI_COMM_WORLD,
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// MPI_STATUS_IGNORE);
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// phreeqc_counts.push_back(phreeqc_tmp, "w" + to_string(p + 1));
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// MPI_Recv(&idle_worker_tmp, 1, MPI_DOUBLE, p + 1, TAG_TIMING,
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// MPI_COMM_WORLD, MPI_STATUS_IGNORE);
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// idle_worker.push_back(idle_worker_tmp, "w" + to_string(p + 1));
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// if (params.dht_enabled) {
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// dht_get_time.push_back(timings[1], "w" + to_string(p + 1));
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// dht_fill_time.push_back(timings[2], "w" + to_string(p + 1));
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// MPI_Recv(dht_perfs, 3, MPI_UNSIGNED_LONG_LONG, p + 1, TAG_DHT_PERF,
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// MPI_COMM_WORLD, MPI_STATUS_IGNORE);
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// dht_hits += dht_perfs[0];
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// dht_miss += dht_perfs[1];
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// dht_collision += dht_perfs[2];
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// }
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// }
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// R.parseEvalQ("profiling <- list()");
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// R["simtime"] = sim_end - sim_start;
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// R.parseEvalQ("profiling$simtime <- simtime");
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// R["simtime_transport"] = cummul_transport;
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// R.parseEvalQ("profiling$simtime_transport <- simtime_transport");
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// R["simtime_chemistry"] = cummul_chemistry;
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// R.parseEvalQ("profiling$simtime_chemistry <- simtime_chemistry");
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// R["simtime_workers"] = master.getWorkerTime();
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// R.parseEvalQ("profiling$simtime_workers <- simtime_workers");
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// R["simtime_chemistry_master"] = master.getChemMasterTime();
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// R.parseEvalQ(
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// "profiling$simtime_chemistry_master <- simtime_chemistry_master");
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// R["seq_master"] = cummul_master_seq;
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// R.parseEvalQ("profiling$seq_master <- seq_master");
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// // R["master_send"] = master_send;
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// // R.parseEvalQ("profiling$master_send <- master_send");
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// // R["master_recv"] = master_recv;
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// // R.parseEvalQ("profiling$master_recv <- master_recv");
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// R["idle_master"] = master.getIdleTime();
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// R.parseEvalQ("profiling$idle_master <- idle_master");
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// R["idle_worker"] = idle_worker;
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// R.parseEvalQ("profiling$idle_worker <- idle_worker");
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// R["phreeqc_time"] = phreeqc_time;
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// R.parseEvalQ("profiling$phreeqc <- phreeqc_time");
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// R["phreeqc_count"] = phreeqc_counts;
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// R.parseEvalQ("profiling$phreeqc_count <- phreeqc_count");
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// if (params.dht_enabled) {
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// R["dht_hits"] = dht_hits;
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// R.parseEvalQ("profiling$dht_hits <- dht_hits");
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// R["dht_miss"] = dht_miss;
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// R.parseEvalQ("profiling$dht_miss <- dht_miss");
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// R["dht_collision"] = dht_collision;
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// R.parseEvalQ("profiling$dht_collisions <- dht_collision");
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// R["dht_get_time"] = dht_get_time;
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// R.parseEvalQ("profiling$dht_get_time <- dht_get_time");
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// R["dht_fill_time"] = dht_fill_time;
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// R.parseEvalQ("profiling$dht_fill_time <- dht_fill_time");
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// }
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// free(timings);
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// if (params.dht_enabled) free(dht_perfs);
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string r_vis_code;
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r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
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R.parseEval(r_vis_code);
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cout << "CPP: Done! Results are stored as R objects into <"
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<< params.out_dir << "/timings.rds>" << endl;
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/*exporting results and profiling data*/
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// std::string r_vis_code;
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// r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
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// R.parseEval(r_vis_code);
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} else { /*This is executed by the workers*/
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ChemWorker worker(¶ms, R, grid, dht_comm);
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// worker.prepareSimulation(dht_comm);
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worker.loop();
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}
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// Rcpp::NumericVector phreeqc_time;
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// Rcpp::NumericVector dht_get_time;
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// Rcpp::NumericVector dht_fill_time;
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// Rcpp::IntegerVector phreeqc_counts;
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// Rcpp::NumericVector idle_worker;
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// int phreeqc_tmp;
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// timings = (double *)calloc(3, sizeof(double));
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// int dht_hits = 0;
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// int dht_miss = 0;
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// int dht_collision = 0;
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cout << "CPP: finished, cleanup of process " << params.world_rank << endl;
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// if (params.dht_enabled) {
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// dht_hits = 0;
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// dht_miss = 0;
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// dht_collision = 0;
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// dht_perfs = (uint64_t *)calloc(3, sizeof(uint64_t));
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// }
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// double idle_worker_tmp;
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// for (int p = 0; p < params.world_size - 1; p++) {
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// /* ATTENTION Worker p has rank p+1 */
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// /* Send termination message to worker */
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// MPI_Send(NULL, 0, MPI_DOUBLE, p + 1, TAG_FINISH, MPI_COMM_WORLD);
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// MPI_Recv(timings, 3, MPI_DOUBLE, p + 1, TAG_TIMING, MPI_COMM_WORLD,
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// MPI_STATUS_IGNORE);
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// phreeqc_time.push_back(timings[0], "w" + to_string(p + 1));
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// MPI_Recv(&phreeqc_tmp, 1, MPI_INT, p + 1, TAG_TIMING, MPI_COMM_WORLD,
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// MPI_STATUS_IGNORE);
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// phreeqc_counts.push_back(phreeqc_tmp, "w" + to_string(p + 1));
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// MPI_Recv(&idle_worker_tmp, 1, MPI_DOUBLE, p + 1, TAG_TIMING,
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// MPI_COMM_WORLD, MPI_STATUS_IGNORE);
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// idle_worker.push_back(idle_worker_tmp, "w" + to_string(p + 1));
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// if (params.dht_enabled) {
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// dht_get_time.push_back(timings[1], "w" + to_string(p + 1));
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// dht_fill_time.push_back(timings[2], "w" + to_string(p + 1));
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// MPI_Recv(dht_perfs, 3, MPI_UNSIGNED_LONG_LONG, p + 1, TAG_DHT_PERF,
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// MPI_COMM_WORLD, MPI_STATUS_IGNORE);
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// dht_hits += dht_perfs[0];
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// dht_miss += dht_perfs[1];
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// dht_collision += dht_perfs[2];
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// if (params.dht_strategy == 0) {
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// if (params.world_rank != 0) {
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// DHT_free(dht_object, NULL, NULL);
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// }
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// } else {
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// DHT_free(dht_object, NULL, NULL);
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// }
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// }
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// R.parseEvalQ("profiling <- list()");
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// free(mpi_buffer);
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MPI_Finalize();
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// R["simtime"] = sim_end - sim_start;
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// R.parseEvalQ("profiling$simtime <- simtime");
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// R["simtime_transport"] = cummul_transport;
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// R.parseEvalQ("profiling$simtime_transport <- simtime_transport");
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// R["simtime_chemistry"] = cummul_chemistry;
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// R.parseEvalQ("profiling$simtime_chemistry <- simtime_chemistry");
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// R["simtime_workers"] = master.getWorkerTime();
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// R.parseEvalQ("profiling$simtime_workers <- simtime_workers");
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// R["simtime_chemistry_master"] = master.getChemMasterTime();
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// R.parseEvalQ(
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// "profiling$simtime_chemistry_master <- simtime_chemistry_master");
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if (params.world_rank == 0) {
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cout << "CPP: done, bye!" << endl;
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}
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// R["seq_master"] = cummul_master_seq;
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// R.parseEvalQ("profiling$seq_master <- seq_master");
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// // R["master_send"] = master_send;
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// // R.parseEvalQ("profiling$master_send <- master_send");
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// // R["master_recv"] = master_recv;
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// // R.parseEvalQ("profiling$master_recv <- master_recv");
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// R["idle_master"] = master.getIdleTime();
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// R.parseEvalQ("profiling$idle_master <- idle_master");
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// R["idle_worker"] = idle_worker;
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// R.parseEvalQ("profiling$idle_worker <- idle_worker");
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// R["phreeqc_time"] = phreeqc_time;
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// R.parseEvalQ("profiling$phreeqc <- phreeqc_time");
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// R["phreeqc_count"] = phreeqc_counts;
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// R.parseEvalQ("profiling$phreeqc_count <- phreeqc_count");
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// if (params.dht_enabled) {
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// R["dht_hits"] = dht_hits;
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// R.parseEvalQ("profiling$dht_hits <- dht_hits");
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// R["dht_miss"] = dht_miss;
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// R.parseEvalQ("profiling$dht_miss <- dht_miss");
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// R["dht_collision"] = dht_collision;
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// R.parseEvalQ("profiling$dht_collisions <- dht_collision");
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// R["dht_get_time"] = dht_get_time;
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// R.parseEvalQ("profiling$dht_get_time <- dht_get_time");
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// R["dht_fill_time"] = dht_fill_time;
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// R.parseEvalQ("profiling$dht_fill_time <- dht_fill_time");
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// }
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// free(timings);
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// if (params.dht_enabled) free(dht_perfs);
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string r_vis_code;
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r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
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R.parseEval(r_vis_code);
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cout << "CPP: Done! Results are stored as R objects into <" << params.out_dir
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<< "/timings.rds>" << endl;
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/*exporting results and profiling data*/
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// std::string r_vis_code;
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// r_vis_code = "saveRDS(profiling, file=paste0(fileout,'/timings.rds'));";
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// R.parseEval(r_vis_code);
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}
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else { /*This is executed by the workers*/
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ChemWorker worker(¶ms, R, grid, dht_comm);
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// worker.prepareSimulation(dht_comm);
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worker.loop();
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}
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cout << "CPP: finished, cleanup of process " << params.world_rank << endl;
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// if (params.dht_enabled) {
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// if (params.dht_strategy == 0) {
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// if (params.world_rank != 0) {
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// DHT_free(dht_object, NULL, NULL);
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// }
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// } else {
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// DHT_free(dht_object, NULL, NULL);
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// }
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// }
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// free(mpi_buffer);
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MPI_Finalize();
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if (params.world_rank == 0) {
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cout << "CPP: done, bye!" << endl;
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}
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exit(0);
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exit(0);
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}
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