chore: Extract benchmark data during CMake configuration

CMakeLists.txt

@@ -14,6 +14,11 @@ add_subdirectory(tug EXCLUDE_FROM_ALL)
 
 add_subdirectory(eval)
 
-add_executable(bench ${GEN_SRC})
+add_executable(bench_FTCS ${GEN_SRC})
-target_link_libraries(bench PRIVATE Eigen3::Eigen tug)
+target_link_libraries(bench_FTCS PRIVATE Eigen3::Eigen tug)
-target_include_directories(bench PRIVATE ${CMAKE_BINARY_DIR}/eval)
+target_include_directories(bench_FTCS PRIVATE ${CMAKE_BINARY_DIR}/eval)
+target_compile_definitions(bench_FTCS PRIVATE BENCH_FTCS)
+
+add_executable(bench_BTCS ${GEN_SRC})
+target_link_libraries(bench_BTCS PRIVATE Eigen3::Eigen tug)
+target_include_directories(bench_BTCS PRIVATE ${CMAKE_BINARY_DIR}/eval)

Readme.md

@@ -6,11 +6,11 @@ This repository contains input data from POET simulations used in the
 NAAICE project and is simulated with the latest version of tug with
 heterogeneous alphas.
 
-Benchmarks (grids, timestep, file paths, etc) are defined in the
+Benchmarks (grids, timestep, file paths, etc) are defined in the header file
-header file `eval/bench_defs.hpp.in`. The data used by the three
+`eval/bench_defs.hpp.in`. The data used by the three benchmarks `barite_200`,
-benchmarks `barite_200`, `barite_large` and `surfex` are in the
+`barite_large` and `surfex` are in the corresponding subdirectories of `eval`,
-corresponding subdirectories of `eval`, as `tar.gz`. Remember to
+as `tar.gz`. Remember to unpack them before running the executable into the
-unpack them before running the executable!
+same directory of the executable. Or just let CMake do it for you.
 
 To write the results to file, set the `BENCH_OUTPUT` environmental
 variable, e.g. `BENCH_OUTPUT=1 ./bench`. The resulting fields are

eval/CMakeLists.txt

@@ -1,5 +1,31 @@
-set(BARITE_200_BENCH "${CMAKE_CURRENT_SOURCE_DIR}/barite_200")
+set(benchmarks
-set(BARITE_LARGE_BENCH "${CMAKE_CURRENT_SOURCE_DIR}/barite_large")
+	"${CMAKE_CURRENT_SOURCE_DIR}/barite_200"
-set(SURFEX_BENCH "${CMAKE_CURRENT_SOURCE_DIR}/surfex")
+	"${CMAKE_CURRENT_SOURCE_DIR}/barite_large"
+	"${CMAKE_CURRENT_SOURCE_DIR}/surfex"
+)
+
+foreach(benchmark ${benchmarks})
+	# find tar.gz files
+	file(GLOB_RECURSE tar_files "${benchmark}/*.tar.gz")
+	foreach(tar_file ${tar_files})
+		# get the name of the tar file
+		get_filename_component(tar_name ${tar_file} NAME_WE)
+		# get the name of the directory
+		get_filename_component(dir_name ${tar_file} DIRECTORY)
+		get_filename_component(dir_name ${dir_name} NAME)
+		# create the directory
+message("Extracting ${tar_name} to ${dir_name}")
+		file(MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/${dir_name}")
+		# extract the tar file
+		execute_process(
+			COMMAND tar -xzf ${tar_file} 
+			WORKING_DIRECTORY "${CMAKE_BINARY_DIR}/${dir_name}"
+		)
+	endforeach()
+endforeach()
+
+set(BARITE_200_BENCH "${CMAKE_BINARY_DIR}/barite_200")
+set(BARITE_LARGE_BENCH "${CMAKE_BINARY_DIR}/barite_large")
+set(SURFEX_BENCH "${CMAKE_BINARY_DIR}/surfex")
 
 configure_file(bench_defs.hpp.in bench_defs.hpp)

eval/bench_defs.hpp.in

@@ -1,9 +1,9 @@
 #ifndef _BENCH_DEFS_HPP
 #define _BENCH_DEFS_HPP
 
+#include <iostream>
 #include <string>
 #include <vector>
-#include <iostream>
 
 struct init_boundary {
   const std::vector<int> north_const;
@@ -31,7 +31,6 @@ struct bench_input {
   const int iterations;
 };
 
-
 static const std::vector<int> gen_vec(int elems) {
   std::vector<int> vec(elems);
   for (int i = 0; i < elems; i++) {
@@ -42,7 +41,7 @@ static const std::vector<int> gen_vec(int elems) {
 }
 
 static const std::vector<int> gen_vec_rev(int from, int to) {
-  int size = to - from+1;
+  int size = to - from + 1;
   std::vector<int> vec(size);
   for (int i = from; i < to; i++) {
     vec[i] = i;
@@ -66,9 +65,8 @@ static bench_input barite_200_input = {
                  .west_const = {0, 1, 2, 3, 4},
                  .values = {111.0124, 55.50622, -3.336970273297e-08, 0.1, 0.2,
                             .0, .0}},
-    .timestep = 1000,
+    .timestep = 500,
-    .iterations = 50
+    .iterations = 100};
-};
 
 static bench_input barite_large_input = {
     .csv_file_init = "@BARITE_LARGE_BENCH@/barite_large_init.csv",
@@ -83,9 +81,8 @@ static bench_input barite_large_input = {
                  .east_const = {},
                  .west_const = {},
                  .values = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0}},
-    .timestep = 100,
+    .timestep = 50,
-    .iterations = 5
+    .iterations = 10};
-};
 
 static bench_input surfex_input = {
     .csv_file_init = "@SURFEX_BENCH@/surfex_init.csv",
@@ -96,58 +93,31 @@ static bench_input surfex_input = {
     .s_x = 0.02,
     .s_y = 0.01,
     .boundary = {.north_const = gen_vec(200),
-		 .south_const = gen_vec(200),
+                 .south_const = gen_vec(200),
                  .east_const = gen_vec(100),
                  .west_const = gen_vec(100),
-                 .values = {120.0,          // H
+                 .values = {120.0,     // H
-			    55.1,	    // O
+                            55.1,      // O
-			    8.0e-17,	    // Charge
+                            8.0e-17,   // Charge
-			    2.0e-15, 	    // CH4
+                            2.0e-15,   // CH4
-			    0.2,            // C
+                            0.2,       // C
-			    0.03,	    // Ca
+                            0.03,      // Ca
-			    0.5,	    // Cl
+                            0.5,       // Cl
-			    0.0002, 	    // Fe2
+                            0.0002,    // Fe2
-			    2.0e-08,	    // Fe3
+                            2.0e-08,   // Fe3
-			    2.0e-11, 	    // H0
+                            2.0e-11,   // H0
-			    1.0e-05,	    // K
+                            1.0e-05,   // K
-			    0.2,	    // Mg
+                            0.2,       // Mg
-			    0.3,	    // Na
+                            0.3,       // Na
-			    0,		    // HS2
+                            0,         // HS2
-			    8.3e-12,	    // S2
+                            8.3e-12,   // S2
-			    5.1e-14, 	    // S4
+                            5.1e-14,   // S4
-			    0.026,	    // S6
+                            0.026,     // S6
-			    0.045,	    // Sr
+                            0.045,     // Sr
-			    2.5e-08,	    // U4
+                            2.5e-08,   // U4
-			    1.6e-10,	    // U5
+                            1.6e-10,   // U5
-			    1.0e-05}},	    // U6
+                            1.0e-05}}, // U6
-    .timestep = 3600,
+    .timestep = 1800,
-    .iterations = 20
+    .iterations = 40};
-};
 
 #endif // _BENCH_DEFS_HPP
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src/main.cpp

@@ -4,8 +4,6 @@
 #include <cstdlib>
 #include <iostream>
 #include <string>
-#include <tug/Simulation.hpp>
-#include <vector>
 
 using TugType = double;
 

src/run.cpp

@@ -1,8 +1,8 @@
 #include "run.hpp"
 
 #include "io.hpp"
-#include "tug/Boundary.hpp"
+#include "tug/Core/Numeric/FTCS.hpp"
-#include "tug/Grid.hpp"
+#include "tug/Diffusion.hpp"
 
 #include <Eigen/src/Core/Map.h>
 #include <Eigen/src/Core/Matrix.h>
@@ -11,7 +11,7 @@
 #include <ratio>
 #include <vector>
 
-#include <tug/Simulation.hpp>
+#include <tug/Core/Matrix.hpp>
 
 #include <Eigen/Eigen>
 
@@ -30,14 +30,19 @@ double run_bench(const bench_input &input, const std::string &output_file) {
   // create tug grids and boundary conditions
   for (int i = 0; i < raw_data.size(); i++) {
 
-    Eigen::Map<RowMajorMat> mat(raw_data[i].data(), input.nrows, input.ncols);
+#ifdef BENCH_FTCS
-    tug::Grid<TugType> grid(input.nrows, input.ncols);
+    tug::Diffusion<TugType, tug::FTCS_APPROACH> diffu(raw_data[i].data(),
+                                                      input.nrows, input.ncols);
+#else
+    tug::Diffusion<TugType, tug::BTCS_APPROACH> diffu(raw_data[i].data(),
+                                                      input.nrows, input.ncols);
+#endif
 
-    grid.setConcentrations(mat);
+    diffu.setDomain(input.s_x, input.s_y);
-    grid.setDomain(input.s_x, input.s_y);
+    diffu.setAlphaX(alpha_x);
-    grid.setAlpha(alpha_x, alpha_y);
+    diffu.setAlphaY(alpha_y);
 
-    tug::Boundary<TugType> boundary(grid);
+    tug::Boundary<TugType> &boundary = diffu.getBoundaryConditions();
 
     // set north boundary
     for (const auto &index : input.boundary.north_const) {
@@ -63,21 +68,15 @@ double run_bench(const bench_input &input, const std::string &output_file) {
                                           input.boundary.values[i]);
     }
 
-    tug::Simulation<TugType> sim(grid, boundary);
-
     if (const char *out = std::getenv("OMP_NUM_THREADS")) {
       int ompNumThreads = std::stoi(out, NULL);
-      sim.setNumberThreads(ompNumThreads);
+      diffu.setNumberThreads(ompNumThreads);
     }
 
-    sim.setTimestep(input.timestep);
+    diffu.setTimestep(input.timestep);
-    sim.setIterations(input.iterations);
+    diffu.setIterations(input.iterations);
 
-    sim.run();
+    diffu.run();
-
-    const auto &result = grid.getConcentrations();
-
-    raw_data[i] = eigenMatrix_to_vector(result);
   }
 
   const auto end_t = std::chrono::high_resolution_clock::now();

tug

@@ -1 +1 @@
-Subproject commit 4867261f9d902ea2be161889a968d3bff519f15c
+Subproject commit 9ca0735654d0ca808fa4704b2b2e13cf417ab865