Enable DHT time measurement

bin/barite_fgcs_2.R

@@ -1,123 +0,0 @@
-## Time-stamp: "Last modified 2024-12-11 16:08:11 delucia"
-
-cols <- 1000
-rows <- 1000
-
-dim_cols <- 50
-dim_rows <- 50
-
-ncirc <- 20 ## number of crystals
-rmax <- cols / 10 ## max radius (in nodes)
-
-set.seed(22933)
-
-centers <- cbind(sample(seq_len(cols), ncirc), sample(seq_len(rows), ncirc))
-radii <- sample(seq_len(rmax), ncirc, replace = TRUE)
-mi <- matrix(rep(seq_len(cols), rows), byrow = TRUE, nrow = rows)
-mj <- matrix(rep(seq_len(cols), each = rows), byrow = TRUE, nrow = rows)
-
-tmpl <- lapply(seq_len(ncirc), function(x) which((mi - centers[x, 1])^2 + (mj - centers[x, 2])^2 < radii[x]^2, arr.ind = TRUE))
-
-inds <- do.call(rbind, tmpl)
-grid <- matrix(1, nrow = rows, ncol = cols)
-grid[inds] <- 2
-
-alpha <- matrix(1e-5, ncol = cols, nrow = rows)
-alpha[inds] <- 1e-7
-
-## image(grid, asp=1)
-
-## Define grid configuration for POET model
-grid_setup <- list(
-  pqc_in_file    = "./barite_fgcs_2.pqi",
-  pqc_db_file    = "../barite/db_barite.dat", ## database file
-  grid_def       = grid, ## grid definition, IDs according to the Phreeqc input
-  grid_size      = c(dim_cols, dim_rows), ## grid size in meters
-  constant_cells = c() ## IDs of cells with constant concentration
-)
-
-bound_length <- cols / 10
-
-bound_N <- list(
-  "type"   = rep("constant", bound_length),
-  "sol_id" = rep(3, bound_length),
-  "cell"   = seq(1, bound_length)
-)
-
-bound_W <- list(
-  "type"   = rep("constant", bound_length),
-  "sol_id" = rep(3, bound_length),
-  "cell"   = seq(1, bound_length)
-)
-bound_E <- list(
-  "type"   = rep("constant", bound_length),
-  "sol_id" = rep(4, bound_length),
-  "cell"   = seq(rows - bound_length + 1, rows)
-)
-
-bound_S <- list(
-  "type"   = rep("constant", bound_length),
-  "sol_id" = rep(4, bound_length),
-  "cell"   = seq(cols - bound_length + 1, cols)
-)
-
-diffusion_setup <- list(
-  boundaries = list(
-    "W" = bound_W,
-    "N" = bound_N,
-    "E" = bound_E,
-    "S" = bound_S
-  ),
-  alpha_x = alpha,
-  alpha_y = alpha
-)
-
-dht_species <- c(
-  "H"         = 7,
-  "O"         = 7,
-  "Ba"        = 7,
-  "Cl"        = 7,
-  "S"         = 7,
-  "Sr"        = 7,
-  "Barite"    = 4,
-  "Celestite" = 4
-)
-
-pht_species <- c(
-  "Ba"        = 4,
-  "Cl"        = 3,
-  "S"         = 3,
-  "Sr"        = 3,
-  "Barite"    = 0,
-  "Celestite" = 0
-)
-
-chemistry_setup <- list(
-  dht_species = dht_species,
-  pht_species = pht_species
-)
-
-## Define a setup list for simulation configuration
-setup <- list(
-  Grid = grid_setup, ## Parameters related to the grid structure
-  Diffusion = diffusion_setup, ## Parameters related to the diffusion process
-  Chemistry = chemistry_setup
-)
-
-
-iterations <- 100
-dt <- 200
-checkpoint_interval <- 20
-control_interval <- 20
-mape_threshold <- rep(3.5e-3, 13)
-#out_save <- seq(50, iterations, by = 50)
-
-
-list(
-    timesteps = rep(dt, iterations),
-    store_result = FALSE,
-    #out_save = out_save,
-    checkpoint_interval = checkpoint_interval,
-    control_interval = control_interval,
-    mape_threshold = mape_threshold
-)

bin/barite_fgcs_2.pqi

@@ -1,49 +0,0 @@
-SOLUTION 1
-  units	mol/kgw
-  water	1
-  temperature	25
-  pH     7.008 
-  pe    10.798
-  S      6.205e-04
-  Sr     6.205e-04
-END
-
-SOLUTION 2
-  units	mol/kgw
-  water	1
-  temperature	25
-  pH     7.008 
-  pe    10.798
-  S      6.205e-04
-  Sr     6.205e-04
-KINETICS 2
-  Barite
-    -m 0.00
-    -parms 50.  # reactive surface area
-    -tol 1e-9
-  Celestite
-    -m 1
-    -parms 10.0  # reactive surface area
-    -tol 1e-9
-END
-
-SOLUTION 3
-  units mol/kgw
-  water 1
-  temperature 25
-  Ba 0.1
-  Cl 0.2
-END
-
-SOLUTION 4
-  units mol/kgw
-  water 1
-  temperature 25
-  Ba 0.2
-  Cl 0.4
-END
-
-
-RUN_CELLS
-  -cells 1 2 3 4
-END

bin/dolo_fgcs_3.R

@@ -115,19 +115,19 @@ setup <- list(
     Chemistry = chemistry_setup # Parameters related to the chemistry process
 )
 
-iterations <- 5000
+iterations <- 15000
 dt <- 200
 checkpoint_interval <- 100
 control_interval <- 100
-mape_threshold <- rep(3.5e-3, 13)
+mape_threshold <- rep(0.1, 13)
 mape_threshold[5] <- 1 #Charge
 out_save <- seq(1000, iterations, by = 1000)
-out_save = c(seq(1, 10), seq(10, 100, by= 10), seq(200, iterations, by=100))
+#out_save = c(seq(1, 10), seq(10, 100, by= 10), seq(200, iterations, by=100))
 
 
 list(
     timesteps = rep(dt, iterations),
-    store_result = FALSE,
+    store_result = TRUE,
     out_save = out_save,
     checkpoint_interval = checkpoint_interval,
     control_interval = control_interval,

bin/run_poet.sh

@@ -1,18 +1,19 @@
 #!/bin/bash
-#SBATCH --job-name=dolo_5000_no_charge
+#SBATCH --job-name=dolo_proto1_eps01
-#SBATCH --output=dolo_5000_no_charge_%j.out
+#SBATCH --output=dolo_proto1_eps01_%j.out
-#SBATCH --error=dolo_5000_no_charge_%j.err
+#SBATCH --error=dolo_proto1_eps01_%j.err
 #SBATCH --partition=long
 #SBATCH --nodes=6                                                    
 #SBATCH --ntasks-per-node=24 
 #SBATCH --ntasks=144                                  
 #SBATCH --exclusive
-#SBATCH --time=12:00:00                             
+#SBATCH --time=3-00:00:00                             
 
 
 source /etc/profile.d/modules.sh
 module purge
 module load cmake gcc openmpi
 
-mpirun -n 144 ./poet --interp dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_5000_no_charge
+#mpirun -n 144 ./poet dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_only_pqc
-##mpirun -n 96 ./poet --interp  barite_fgcs_2.R barite_fgcs_2.qs2 bar_warmup
+mpirun -n 144 ./poet --interp dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_proto1_eps01
+#mpirun -n 144 ./poet --interp  barite_fgcs_4_new/barite_fgcs_4_new_rt.R barite_fgcs_4_new/barite_fgcs_4_new.qs2 barite

src/Control/ControlModule.cpp

@@ -39,13 +39,13 @@ void poet::ControlModule::initiateWarmupPhase(bool dht_enabled,
     chem->SetWarmupEnabled(true);
     chem->SetDhtEnabled(false);
     chem->SetInterpEnabled(false);
-   // MSG("Warmup enabled until next control interval at iteration " +
+    MSG("Warmup enabled until next control interval at iteration " +
-     //   std::to_string(control_interval) + ".");
+        std::to_string(control_interval) + ".");
 
     if (rollback_enabled) {
       if (sur_disabled_counter > 0) {
         --sur_disabled_counter;
-        //MSG("Rollback counter: " + std::to_string(sur_disabled_counter));
+        MSG("Rollback counter: " + std::to_string(sur_disabled_counter));
       } else {
         rollback_enabled = false;
       }
@@ -64,16 +64,17 @@ void poet::ControlModule::applyControlLogic(ChemistryModule &chem,
     return;
   }
   writeCheckpointAndMetrics(chem, iter);
-
+  
-  if (checkAndRollback(chem, iter) /* && rollback_count < 4*/) {
+  if (checkAndRollback(chem, iter)  && rollback_count < 3) {
     rollback_enabled = true;
     rollback_count++;
     sur_disabled_counter = control_interval;
-    /*
+
     MSG("Interpolation disabled for the next " +
         std::to_string(control_interval) + ".");
-    */
+    
   }
+  
 }
 
 void poet::ControlModule::writeCheckpointAndMetrics(ChemistryModule &chem,

src/poet.cpp

@@ -439,13 +439,13 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
       Rcpp::wrap(chem.GetWorkerControlTimings());
       
 
-  if (params.use_dht) {
+  //if (params.use_dht) {
     chem_profiling["dht_hits"] = Rcpp::wrap(chem.GetWorkerDHTHits());
     chem_profiling["dht_evictions"] = Rcpp::wrap(chem.GetWorkerDHTEvictions());
     chem_profiling["dht_get_time"] = Rcpp::wrap(chem.GetWorkerDHTGetTimings());
     chem_profiling["dht_fill_time"] =
         Rcpp::wrap(chem.GetWorkerDHTFillTimings());
-  }
+  //}
 
   if (params.use_interp) {
     chem_profiling["interp_w"] =